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- set -e
- function usage() {
- echo "Usage: $0 [ -r <Result_dir> ] [ -o <out_dir> ] [ -l <sam_list> ] [ -x <script_dir> ] [ -c <WES_CNV_outdir> ]"
- echo "-r Final result dir"
- echo "-o Output dir"
- echo "-l sample list"
- echo "-x script_dir"
- echo "-c WES CNV outdir"
- }
- if [ $# -eq 0 ]
- then
- usage
- exit
- fi
- while getopts ":r:o:l:x:c:h" opt; do
- case $opt in
- r)
- res_dir=$OPTARG
- ;;
- o)
- out_dir=$OPTARG
- ;;
- l)
- sam_list=$OPTARG
- ;;
- c)
- cnv_dir=$OPTARG
- ;;
- x)
- script_dir=$OPTARG
- ;;
- h)
- usage
- exit
- ;;
- \?)
- echo "Invalid option: -$OPTARG" > /dev/stderr
- usage
- exit
- ;;
- esac
- done
- . $script_dir/conf/conf.cfg
- echo "Result Dir:" $res_dir
- echo "CNV analysis Dir:" $cnv_dir
- echo "Output outDir:" $out_dir
- ## keyan-Male
- echo -e "\n"
- echo "Male:"
- test -d $res_dir/keyan || mkdir $res_dir/keyan
- test -d $out_dir/keyan || mkdir $out_dir/keyan
- cd $out_dir/keyan
- for sample in `cut -f1 $sam_list`
- do
- cp $out_dir/${sample}/${sample}.gatk.hg19_multianno.txt .
- cp $cnv_dir/${sample}.CNV.xls .
- done
- perl $keyan_dir/filter_loop_v5.pl $MKY_genelist
- chmod g-w Lib*.xls
- rm *.hg19_multianno.txt *.CNV.xls
- for sample in `cut -f1 $sam_list`
- do
- lib=`echo $sample|cut -d- -f2`
- cp $lib.filter_raw.xls $res_dir/keyan/$lib.filter_raw.xls
- cp $lib.filter_recessive.xls $res_dir/keyan/$lib.filter_recessive.xls
- done
- ## keyan-Female
- echo -e "\n"
- echo "Female:"
- test -d $res_dir/keyan-F || mkdir $res_dir/keyan-F
- test -d $out_dir/keyan-F || mkdir $out_dir/keyan-F
- cd $out_dir/keyan-F
- for sample in `cut -f1 $sam_list`
- do
- cp $out_dir/${sample}/${sample}.gatk.hg19_multianno.txt .
- cp $cnv_dir/${sample}.CNV.xls .
- done
- perl $keyan_dir/filter_loop_female_V1.pl $FKY_genelist
- chmod g-w Lib*.xls
- rm *.hg19_multianno.txt *.CNV.xls
- for sample in `cut -f1 $sam_list`
- do
- lib=`echo $sample|cut -d- -f2`
- cp $lib.filter_raw.xls $res_dir/keyan-F/$lib.filter_raw.xls
- cp $lib.filter_recessive.xls $res_dir/keyan-F/$lib.filter_recessive.xls
- done
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